Align D-mannose and D-mannitol transporter (characterized)
to candidate BPHYT_RS23445 BPHYT_RS23445 hexuronate transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__BFirm:BPHYT_RS23445 Length = 430 Score = 460 bits (1184), Expect = e-134 Identities = 223/422 (52%), Positives = 299/422 (70%), Gaps = 21/422 (4%) Query: 1 MFGQGRSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFN 60 M R ++ +LFLAGVINYLDR+ALS+AAP IQKD S +MG++FSSFF+GYA FN Sbjct: 1 MIKSQRWFVVALLFLAGVINYLDRAALSIAAPLIQKDLNFSHAQMGIVFSSFFIGYALFN 60 Query: 61 FIGGWAADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKM 120 F+GG +D+ GAK AM +WS+F G T L G SL+++R+LFGMGEGP S + SKM Sbjct: 61 FVGGVLSDKVGAKRVFGTAMGVWSVFCGATALATGIGSLIVLRVLFGMGEGPFSSSNSKM 120 Query: 121 VNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWF 180 VNNW+ K A AIG SGTPLGGA++GPVVGF+AV +GW+ +F+ IML+GL+W +W Sbjct: 121 VNNWFPRKEVASAIGVISSGTPLGGALAGPVVGFMAVQFGWRWAFVAIMLLGLLWLVLWA 180 Query: 181 KFVKERPE---------------GEGAEDILRAEGQGELAAQPVFPLRFYLKQPTVLFTS 225 E P G+ E + GE LR +L++P +L T+ Sbjct: 181 ATTTEHPHQNSRITPDEIELIRAGQADEHAIAHSASGERLG-----LRHFLRKPIILATA 235 Query: 226 LAFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKK 285 AFFSYNY LFFFL+WFP+YLT AH L+++DMS ATVIPW+LG +GLA GGFISDF+ + Sbjct: 236 FAFFSYNYVLFFFLSWFPTYLTEAHHLSLRDMSFATVIPWLLGSIGLAAGGFISDFILRL 295 Query: 286 TGRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDT 345 TG+ + SRK+VL +CL A AVC+A AG V + AV L+++++FFLY+TGA+YWA+IQDT Sbjct: 296 TGKPLLSRKLVLGSCLGAAAVCVALAGRVASTQGAVALMSVSIFFLYVTGAVYWAVIQDT 355 Query: 346 VPAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFT-GSFTSAFLLAGLLTVIGAVCVARY 404 VP VGGV GF+H LAN +G++GP +TGF+V+ T G++ SAF+LAG++ V+GAVC + Sbjct: 356 VPREHVGGVGGFVHLLANLAGVIGPAVTGFIVEATHGNYASAFVLAGVIAVLGAVCSLVW 415 Query: 405 VK 406 ++ Sbjct: 416 IR 417 Lambda K H 0.329 0.142 0.439 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 632 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 430 Length of database: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory